#
# SPDX-License-Identifier: Apache-2.0
+from past.builtins import basestring
+from future.utils import viewitems
+
import os
import json
import copy
import ruamel.yaml as yaml
from .runner import (upload_dependencies, packed_workflow, upload_workflow_collection,
- trim_anonymous_location, remove_redundant_fields, discover_secondary_files)
+ trim_anonymous_location, remove_redundant_fields, discover_secondary_files,
+ make_builder)
from .pathmapper import ArvPathMapper, trim_listing
-from .arvtool import ArvadosCommandTool, set_cluster_target, make_builder
+from .arvtool import ArvadosCommandTool, set_cluster_target
+
from .perf import Perf
logger = logging.getLogger('arvados.cwl-runner')
runtimeContext = runtimeContext.copy()
runtimeContext.toplevel = True # Preserve behavior for #13365
- builder = make_builder({shortname(k): v for k,v in joborder.items()}, self.hints, self.requirements, runtimeContext)
+ builder = make_builder({shortname(k): v for k,v in viewitems(joborder)}, self.hints, self.requirements, runtimeContext)
runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
return super(ArvadosWorkflowStep, self).job(joborder, output_callback, runtimeContext)
raise WorkflowException("%s object must have 'id'" % (self.tool["class"]))
document_loader, workflowobj, uri = (self.doc_loader, self.doc_loader.fetch(self.tool["id"]), self.tool["id"])
- discover_secondary_files(self.tool["inputs"], joborder)
+ discover_secondary_files(self.arvrunner.fs_access, builder,
+ self.tool["inputs"], joborder)
with Perf(metrics, "subworkflow upload_deps"):
upload_dependencies(self.arvrunner,
adjustDirObjs(packed, keepmount)
self.wf_pdh = upload_workflow_collection(self.arvrunner, shortname(self.tool["id"]), packed)
+ self.loadingContext = self.loadingContext.copy()
+ self.loadingContext.metadata = self.loadingContext.metadata.copy()
+ self.loadingContext.metadata["http://commonwl.org/cwltool#original_cwlVersion"] = "v1.0"
+
wf_runner = cmap({
"class": "CommandLineTool",
"baseCommand": "cwltool",